I played a little with pyPdf to set the page margins. Below are some test codes for creating PDF files with flat pages, setting the multimedia box and the trim box in the upper right to the same as on the first page, which could be the starting point for something more useful.
from pyPdf import PdfFileWriter, PdfFileReader
from pdfsave import pdfSave
import sys
def pdfSetBoxes(input, output, mediaBox, cropBox):
numPages = input.getNumPages()
for pageNum in range(1,numPages, 2):
page = input.getPage(pageNum)
page.mediaBox.upperRight = mediaBox
page.cropBox.upperRight = cropBox
output.addPage(page)
input = PdfFileReader(file(sys.argv[1], "rb"))
output = PdfFileWriter()
page0 = input.getPage(0)
mb = page0.mediaBox.getUpperRight()
cb = page0.cropBox.getUpperRight()
pdfSetBoxes(input, output, mb, cb)
pdfSave(output, sys.argv[2])